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Flashcards by Abigail Leslie, updated 9 months ago
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Created by Abigail Leslie
10 months ago
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| Question | Answer |
| Upstream (negative numbers) | Nomenclature, DNA on the template/nontemplate strand that is before the initiation point of transcription |
| Downstream (positive numbers) | Nomenclature, DNA on the template/nontemplate strand that is before the initiation point of transcription |
| Template Strand | The DNA strand that is being used to synthesis mRNA |
| Nontemplate Strand | The DNA strand that is not being used to synthesize RNA, and is attached to the Template strand |
| Promoter | Site of transcription initiation |
| Enhancer | Eukaryotes - site on DNA where transcription factors bind. More distant than in bacteria |
| Operator | Bacteria - Site where transcription factors bind. Closer than in Eukaryotes |
| Terminator | Site of transcription termination |
| Steps of Initiation | 1. Start: RNA polymerase binds promoter 2. RNA pol separates DNA strands - txn bubble 3. First few NTPs (rNTPs) added 4. RNA pol moves past the promoter and changes conformation to be more stably associated with the DNA |
| 1. Start: RNA polymerase binds promoter 2. RNA pol separates DNA strands - txn bubble 3. First few NTPs (rNTPs) added 4. RNA pol moves past the promoter and changes conformation to be more stably associated with the DNA | List the steps of Initiation |
| Elongation | RNA pol moves along the DNA and adds ribonucleotides • Unwinds DNA ahead of it, and DNA repairs • Short region of transcript is paired with DNA; the rest of the RNA is extruded from the polymerase |
| Termination | • RNA pol meets terminator sequence • Dissociates from the DNA |
| RNA Pol I | Which RNA Pol is associated with ribosomal RNA (rRNA)? |
| RNA Pol II | Which RNA Pol is associated with mRNA? |
| RNA Pol III | Which RNA Pol is associated with tRNA? |
| Subunits assemble into a complex with jaw-like lobes, with the active site at the base of the cleft | Describe the structure of RNA pol |
| 2 MG+s prepare the oncoming 3' OH by stabilizing O-, and stabilize the pyrophosphate intermediate. | Describe how RNA pol catalyzes nucleotide addition. How is this similar to DNA Pol? |
| True | True/False: RNA pol II couples mRNA synthesis to mRNA processing? |
| General Transcription Factors | RNA Pols need these extra proteins to target the core enzyme to promoter regions |
| Pre-Initiation Complex (PIC) | TFII Proteins assemble with RNA Pol II to form this |
| TFII | These transcription factors are associated with RNA Pol II |
| TATA Box | A common Promoter motif for RNA Pol II |
| TATA Binding Protein (TBP) | Eukaryotic polymerases need this protein to initiate transcription. It is a part of TFIID |
| TFIID | The binding of this element to the TATA box is the first step in initiation. |
| TBP-associated Factors (TAFs) | These mediate the recognition of other promoter elements, like INR and DPE |
| TFIIB | This element is recruited AFTER TFIID, and helps to determine the transcription direction |
| TFIIA | Binds AFTER TFIID and TFIIB, this element binds and stabilizes TBP-DNA interactions |
| TFIIE and TFIIH | These two elements bind last, after TFIIA, TFIIB, and TFIID |
| TFIIH | This transcription factor binds last AND catalyzes the ATP powered unwinding of DNA |
| Topoisomerase (TXN) | This enzyme creates transient cuts in DNA in order to relieve torsional stress. |
| Closed Complex | RNA pol (complex) + promoter (dsDNA) |
| Open Complex | RNA pol + open DNA |
| Abortive Initiation | This failure occurs frequently in transcription, due to the TFIIB loop being in the way |
| Promoter Clearance | Displacement of the TFIIB loop caused by phosphorylation of TFIIH |
| TFIIH on SER5 | Kinase activity of this enzyme on this residue starts elongation and recruits capping enzyme |
| P-TEFb on SER2 | Kinase activity of this enzyme on this residue resolves pausing after capping. (And is promoted by capping) |
| Transcriptional Pausing | RNA polymerase stops during elongation due to a physical barrier. This is called: |
| Transcriptional arrest | When elongation has paused, and RNA synthesis cannot resume |
| Backtracking | Can be caused by pausing -Most recent RNA protrudes from front of complex -the reverse polymerization reaction occurs (cleavage) This is thought to have a role in error correction |
| FACT | (Facilitates Chromatin Transcription) |
| 1. Release transcript at proper intervals 2. Release the DNA | What must RNA pol do at time of termination? |
| Terminator Sequences | In DNA, these are the signal to cease transcription |
| CPSF | What cleaves the RNA after a terminator sequence? |
| False | True/False: After RNA is cleaved, RNA pol stops transcription |
| Allosteric model of RNA pol termination | -RNA processing proteins associate with the processing signals and the CTD -Cleavage or recognition of processing proteins -> conformational changes, Pol II dissociates from DNA |
| Torpedo model of RNA pol termination | After cleavage, the RNA downstream of the poly(A) signal is digested by a 5′ to 3′ endonuclease (Rat1) • Rat1 degrades the nascent RNA until it runs into the RNA polymerase, disrupting polymerization and causing RNA pol to dissociate from the DNA |
| Transcriptional Regulation | What causes •Differentiation and development • Time • Cell type • Environmental changes |
| Repressor | Regulatory protein that decreases transcription |
| Activators | Regulatory proteins that increase transcription |
| Regulatory sequence | Specific DNA in which regulatory proteins bind |
| Operator sites | Regulatory sequences in bacteria are called ____ and are located close to the promoter |
| Enhancers | Regulatory sequences in Eukaryotes are called ____, are often more distal and can be located either upstream or downstream from the gene. |
| Co-activator/Co-repressor | Cannot regulate/bind on their own, must be recruited by activators/repressors |
| DNA binding domain | Domain in activator/repressor that bind DNA. |
| Allosteric binding Modification Abundance/Localization | What can affect TFs |
| Mediatior - Brings enhancer regions closer to the Initiation Site | What is 'required' for transcription? How does it work? |
| Direct interaction, by preventing an activator from binding to an enhancer region | How does direct interaction work for repression? |
| Repressors can recruit other enzymes such as HDACs to prevent transcription | How does recruitment work for repression? |
| 1. OCT4, 2. Sox2, 3. Klf4, 4, c-Myc Are four factors that are critical for cell differentiation. | What are the OSKM factors? What do they do? |
| They are often localized to tissues and low in abundance | What is true about the abundance of sequence specific TFs? |
| An activating/repressing domain and a DNA-binding domain | What domains does a specific sequence TF have? |
| Interacts with major groove, First helix separated from recognition helix by short linker. An example is Homeodomain | What is a helix-turn-helix DNA binding domain? |
| An example of HTH DBD, a monomer. N-terminal interacts with major groove. | What is Homeodomain? |
| A DBD where an alpha helix and 2 beta sheets surround a central zinc atom. Most common, and many proteins have mutliple | What is a Zinc finger? |
| Long alpha helices, dimers. 2 options, 1. coiled coils, and 2. splayed N-term helices that sit in the major groove. | What is a (leucine) zipper? |
| The basic region is disordered | What happens when a zipper isn't bound to DNA? |
| A master TF controls cell identity | What is a Master TF? |
| A set of TFs that can form both Homo and Hetero dimers. | What is Fos/Jun |
| Fos/Jun heterodimer = AP1 • Proliferation (cell growth and division) • S phase genes have AP1 enhancers | What is the Fos/Jun heterodimer used for>? |
| Similar to bZIP • Dimerization often is a leucine zipper, always hydrophobic | What is the difference in a helix-loop-helix DBD? |
| open chromatin | Poised promoter |
| The Max/Myc heterodimer is the active transcription factor. To prevent transcription, Mad sequesters Max, making the dimer unable to form. | How does the Mad/Max heterodimer work? |
| [Trp] low = genes are transcribed • [Trp] high = Trp repressor binds to Trp operator and blocks RNA polymerase from binding • Dependent on high [Trp] | What is the mechanism behind the Trp repressor? |
| Elk-1 is an example of mediator recruitment in Eukaryotes | What is ELK-1 an example of? |
| Mitogen absence: ELK1 binds to DNA and serum response factor (SRF), but doesn’t activate transcription Mitogen presence: Kinases phosphorylate ELK1, which then recruits Mediator | How does Elk-1 respond to Mitogen? |
| Gal4 is an example of mediator recruitment in Eukaryotes, and coregulation | What is Gal4 an example of? |
| When Galactose levels are low, Gal80 bind to Gal4, causing Mediator to not be recruited, When Galactose levels are high, Gal3 sequesters Gal80, and Mediator is recruited | How does Gal80 and Gal3 regulate Gal4? |
| Gal4 was edited several times, and transcription was tested. When the DBD or activating regions were removed, no transcription occurred. When the activation region was removed, but a modified Gal80 with an activating region was added, transcription occurred. | How was it proven that the DBD and activation site of Gal4 are independent? |
| Common in activation domains, and are a large cluster of amino acids that are acidic and largely hydrophobic | What is an acid blob? |
| Production of HSP70. When transcription occurs, activation occurs normally but the regulation is at the transition to elongation, saving the cell both energy (not transcribing) and time (having parts in place) | What is the Heat Shock response? |
| It is the response of a gene to multiple transcription factors/regulatory subunits. | What is combinatorial control? |
| a and (a) (alpha) cells, and the a/(a) haploid | What are the three types of yeast cells? |
| a1, (a)1, (a)2, and MCM1 | What are the genes that control yeast cells? |
| MCM1 | Which gene that controls yeast type is always present? |
| MCM1, which controls the production of a genes | What TFs are activated in an a type yeast cell |
| (a)2 repressed a genes, (a)1 activates (a) genes | What TFs are activated in an (a) type yeast cell, and what do they do? |
| a1 and (a)2 genes form a heterodimer, and repressed haploid genes, including (a)1 | What TFs are activated in an a/(a) haploid? |
| HMG proteins increase flexibility in DNA it is bound to. | What do HMG proteins do? |
| An activator that uses CCCTC binding factor, and regulates chromatin structure. CTCF is an insulator | What is CTCF? |
| Cohesion is a protein ring that works with CTCF. DNA passes through this ring. This creates a chromatin loop | What is cohesion? (the protein) |
| A protein that binds to a ligand effector, and typically have a DBD and a ligand binding domain. Typically Homo or hetero dimers. Spacing determines specificity | What is a nuclear hormone receptor? |
| 1. Escape HSP90 and enter the nucleus or 2. Activate coregulators | What are the two types/mechanisms of Nuclear Hormone Receptors |
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